bio-pathway-enrichment-visualization

Scope

This skill covers enrichplot package functions designed for clusterProfiler results:

• dotplot(), barplot() - Summary views
• cnetplot(), emapplot(), treeplot() - Network/hierarchical views
• gseaplot2(), ridgeplot() - GSEA-specific
• goplot(), heatplot(), upsetplot() - Specialized views

For custom ggplot2 enrichment dotplots (manual implementation), see data-visualization/specialized-omics-plots.

Setup

Goal: Load required packages for visualizing enrichment analysis results.

Approach: Import clusterProfiler, enrichplot, and ggplot2 which provide the plotting functions for enrichment objects.

library(clusterProfiler)
library(enrichplot)
library(ggplot2)

## Dot Plot

**Goal:** Summarize enrichment results showing gene ratio, count, and significance in a single figure.

**Approach:** Use enrichplot dotplot which maps gene ratio to x-axis, term to y-axis, dot size to count, and color to p-value.

Most common visualization - shows gene ratio, count, and significance.

```r
dotplot(ego, showCategory = 20)